brainglobe-registration

v0.0.5

A napari plugin for registration to a BrainGlobe atlas. For more information about how to use this package see README

Latest version published 3 months ago

License: BSD-3-Clause

PyPI

GitHub

Package Health Score

66 / 100

security
No known security issues
popularity
Limited
maintenance
Sustainable
community
Sustainable

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relativity
47

Popularity

Limited

GitHub Stars: 24
Forks: 9
Contributors: 10

Direct Usage Popularity

Based on project statistics from the GitHub repository for the PyPI package brainglobe-registration, we found that it has been starred 24 times.

Security

No known security issues

Security and license risk for latest version

Release Date: Sep 2, 2025
Direct Vulnerabilities: 0
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0
H
0
M
0
L
Indirect Vulnerabilities: 0
C
0
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0
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0
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License Risk: 0
H
0
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All security vulnerabilities belong to production dependencies of direct and indirect packages.

License

BSD-3-Clause

Security Policy

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Maintenance

Sustainable

Commit Frequency

Open Issues: 17
Open PR: 2
Last Release: 3 months ago
Last Commit: 10 days ago

Further analysis of the maintenance status of brainglobe-registration based on released PyPI versions cadence, the repository activity, and other data points determined that its maintenance is Sustainable.

We found that brainglobe-registration demonstrates a positive version release cadence with at least one new version released in the past 12 months.

As a healthy sign for on-going project maintenance, we found that the GitHub repository had at least 1 pull request or issue interacted with by the community.

Community

Sustainable

Readme: Yes
Contributing.md: No
Code of Conduct: Yes
Contributors: 10
Funding: No

This project has seen only 10 or less contributors.

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Package

Python Versions Compatibility: >=3.11

Age: 11 months
Latest Release: 3 months ago
Dependencies: 15 Direct
Versions: 5
Maintainers: 0
Wheels: OS Independent

Readme

brainglobe-registration

Registration to a BrainGlobe atlas using Elastix

> [!WARNING] > This tool is in very early development. The interface may change and some features are not yet available.

A napari plugin for registering images to a BrainGlobe atlas.

brainglobe-registration

Usage

Open napari.
Install the plugin.
Open the widget by selecting Plugins > BrainGlobe Registration in the napari menu bar near the top left of the window. The BrainGlobe Registration plugin will appear on the right hand side of the napari window.
Open the image you want to register in napari (a sample 2D image can be found by selecting File > Open Sample > Sample Brain Slice).
Select the atlas you want to register to from the dropdown menu. The atlas will appear in the napari viewer. Select the approximate Z slice of the atlas that you want to register to, using the slider at the bottom of the napari viewer.
Adjust the sample image to roughly match the atlas image. You can do this by adjusting X and Y translation as well as rotating around the centre of the image. You can overlay the two images by toggling Grid mode in the napari viewer (Ctrl+G). You can then adjust the color map and opacity of the atlas image to make manual alignment easier. The sample image can be reset to its original position and orientation by clicking Reset Image in the BrainGlobe Registration plugin window.
Select the transformations you want to use from the dropdown menu. Set the transformation type to empty to remove a step. Select from one of the three provided default parameter sets (elastix, ARA, or IBL). Customise the parameters further in the Parameters tab.
Click Run to register the image. The registered image will appear in the napari viewer.

Installation

We strongly recommend to use a virtual environment manager (like conda or venv). The installation instructions below will not specify the Qt backend for napari, and you will therefore need to install that separately. Please see the napari installation instructions for further advice on this.

You can install brainglobe-registration via pip:

pip install brainglobe-registration

or via napari.

To install the latest development version :

pip install git+https://github.com/brainglobe/brainglobe-registration.git

License

Distributed under the terms of the BSD-3 license, "brainglobe-registration" is free and open source software

Seeking help or contributing

We are always happy to help users of our tools, and welcome any contributions. If you would like to get in contact with us for any reason, please see the contact page of our website.

Citation

If you find this package useful, and use it in your research, please cite the following: > Igor Tatarnikov, Alessandro Felder, Kimberly Meechan, & Adam Tyson. (2025). brainglobe/brainglobe-registration. Zenodo. https://doi.org/10.5281/zenodo.14750325

Acknowledgements

This napari plugin was generated with Cookiecutter using @napari's cookiecutter-napari-plugin template.

brainglobe-registration dependencies

bayesian-optimization brainglobe-atlasapi dask dask-image fancylog itk-elastix lxml-html-clean numpy pandas pytransform3d qt-niu qtpy scikit-image scipy tifffile

FAQs

What is brainglobe-registration?

A napari plugin for registration to a BrainGlobe atlas. Visit Snyk Advisor to see a full health score report for brainglobe-registration, including popularity, security, maintenance & community analysis.

Is brainglobe-registration popular?

We’re still processing downloads data for the python package brainglobe-registration. Visit the popularity section on Snyk Advisor to see the full popularity analysis.

Is brainglobe-registration well maintained?

We found indications that brainglobe-registration maintenance is sustainable demonstrating some project activity. We saw a total of 10 open source contributors collaborating on the project. See the full package health analysis to learn more about the package maintenance status.

Is brainglobe-registration safe to use?

The python package brainglobe-registration was scanned for known vulnerabilities and missing license, and no issues were found. Thus the package was deemed as safe to use. See the full health analysis review.

Last updated on 12 December-2025, at 01:57 (UTC).

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Readme

brainglobe-registration

Usage

Installation

License

Seeking help or contributing

Citation

Acknowledgements

brainglobe-registration dependencies

FAQs

What is brainglobe-registration?

Is brainglobe-registration popular?

Is brainglobe-registration well maintained?

Is brainglobe-registration safe to use?

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Source Code

Open Source

Container

Config

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